[gmx-users] velacc & box of water

[Jamie Seyed]

Dear Gmx users,
Does any one know why genbox stops when I use this command:
"genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top"
or when I use this command:
"genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top"
It goes until
Reading solvent configuration
Solvent configuration contains 648 atoms in 216 residues
and then stops....
Would you please let me know why it happens?? Many Thanks in Advance/Jamie



On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed <jamie.seyed at gmail.com> wrote:

> Thanks to Justin & Mark for answering my second question...
> Could any one give me a hint on my first question that I copy it again?
> --about g_velacc and calculating the diffusion constant from that. In
> mailing list people say that we need to divide it by mass squared and 1/3.
> Then I found another recent post that said it has been included in the
> code... Would you please clarify this that if I need the factors or not.
> Also I found 2 numbers after integration.
> Integral   1   0.01595
> set    average
> SS1   3.718082e-04
> Would you please inform me what are these number and what is the relation
> between them?
> Many Thanks in Advance/Jamie
>
>   On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul <jalemkul at vt.edu>wrote:
>
>>
>>
>> Jamie Seyed wrote:
>>
>>> Dear Gmx Users,
>>> I have a 2 questions. First about g_velacc and calculating the diffusion
>>> constant from that. In mailing list people say that we need to divide it by
>>> mass squared and 1/3. Then I found another recent post that said it has been
>>> included in the code... Would you please clarify this that if I need the
>>> factors or not. Also I found 2 numbers after integration.
>>> Integral   1   0.01595
>>> set    average
>>> SS1   3.718082e-04
>>> --1) Would you please inform me what are these number and what is the
>>> relation between them?
>>>
>>>
>>
>> Can't comment on the first part...maybe the code will point you in the
>> right direction?
>>
>> --2) My second question is I want to make a box of only water (spce) with
>>> let say 500 water molecules. Would you please give me quick hints how to do
>>> it (the proper way) or refer me to good point? Up to now I can only have 216
>>> water molecules from tuto/water folder and I tried a lot
>>>
>>
>> This task might be approached in a couple of ways:
>>
>> 1. genconf -nbox to define a suitable number of replicate systems.
>> 2. genbox -box -maxsol 500 to define a suitably-sized box and fill it with
>> only the desired number of molecules.
>>
>> -Justin
>>
>>  to start from the beginning, but I could not make it... I appreciate if
>>> you help me to understand the first issue and be able to overcome the second
>>> one. Many Thanks in Advance/Jamie
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
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>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>>
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